Display omitted •The contamination of a carbonated aquifer underlying an old waste disposal site was studied.•The contaminant plume is attenuating, declining its mineralization and chloride content.•Carbonate minerals dissolution would occur in the most contaminated portion of the aquifer.•High leachate HCO3– content acts as a buffer, preventing pH from declining due to CO2 presence.•Dissolution conduits in the karst system, due to contamination, would increase. Hydrogeochemical tools were applied to evaluate the effect caused by the presence of municipal waste leachate on the balance of a karstic aquifer. The system evaluated correspond to the aquifer underlying the area of the old municipal waste disposal site (MWDS) in the city of Merida, Mexico. A contaminant plume identified with chloride ion concentrations was detected. Groundwater samples were collected from boreholes located along a flow line, starting at the downstream boundary of the dump site. The parameters involved in the carbonate system were analyzed, obtaining a decline in calcium (Ca2+) and magnesium (Mg2+) concentrations for high pCO2 values. This behavior is explained by the presence of high bicarbonate (HCO3–) content, as a result of the waste decomposition reactions. The bicarbonate ions behaved as a buffer preventing pH reduction. In addition to this, the calcium and magnesium species indicate that the formation of complexes affected the mineral solubility where leachate has the greatest influence. The transport of minerals, in moles, between boreholes located along the groundwater flow line, was determined through inverse modeling. It is concluded that the leachate affects the carbonate balance, as determined by the transfer of minerals along the flow line; it was observed that mixed waters with a higher percentage of leachate tend to dissolve carbonate minerals. This is the analogous to findings reported in other leachate contaminated aquifers.